Beta-hexosaminidase has become a paradigm for the understanding of lysosomal enzyme biology. In order to gain further insight into the hexosaminidase system, we have isolated human genomic clones covering the entire gene encoding the alpha chain of the enzyme. These clones have been characterized by restriction mapping, Southern blotting and DNA sequencing. The alpha chain gene spans 35 kilobases of DNA and is split into 14 exons. The position of introns matches potential protein processing sites, indicating a correlation of gene structure with protein structure. The promoter region of this gene contains conventional "TATA" and "CAAT" motifs. We have also isolated cDNA and genomic clones encoding the beta chain of hexosaminidase. Sequence analysis of these clones indicate extensive structural homology with the alpha chain with significant differences at the amino-termini of the two subunits.